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<title>Per Base Sequence Content</title>
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<h1>Per Base Sequence Content</h1>
<h2>Summary</h2>
<p>
Per Base Sequence Content plots out the proportion of each base
position in a file for which each of the four normal DNA bases
has been called.
</p>
<p><img src="per_base_sequence_content.png"></p>
<p>
In a random library you would expect that there would be little
to no difference between the different bases of a sequence run, so
the lines in this plot should run parallel with each other.  The
relative amount of each base should reflect the overall amount of
these bases in your genome, but in any case they should not be
hugely imbalanced from each other.
</p>
<p>
If you see strong biases which change in different bases then this 
usually indicates an overrepresented sequence which is contaminating
your library.  A bias which is consistent across all bases either
indicates that the original library was sequence biased, or that there
was a systematic problem during the sequencing of the library.
</p>

<h2>Warning</h2>
<p>
This module issues a warning if the difference between A and T, or G
and C is greater than 10% in any position.
</p>

<h2>Failure</h2>
<p>
This module will fail if the difference between A and T, or G and C
is greater than 20% in any position.
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